HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies

The key requirement for successful immunochemical assay is the availability of antibodies with high specificity and desired affinity. Small molecules, when used as haptens, are not immunogenic. However, on conjugating with carrier molecule they elicit antibody response. The production of anti-hapten antibodies of desired specificity largely depends on the hapten design (preserving greatly the chemical structure and spatial conformation of target compound), selection of the appropriate carrier protein and the conjugation method. This manuscript describes a curated database HaptenDB, where information is collected from published literature and web resources. The current version of the database has 2021 entries for 1087 haptens and 25 carrier proteins, where each entry provides comprehensive details about (1) nature of the hapten, (2) 2D and 3D structures of haptens, (3) carrier proteins, (4) coupling method, (5) method of anti-hapten antibody production, (6) assay method (used for characterization) and (7) specificities of antibodies. The current version of HaptenDB covers a wide array of haptens including pesticides, herbicides, insecticides, drugs, vitamins, steroids, hormones, toxins, dyes, explosives, etc. It provides internal and external links to various databases/resources to obtain further information about the nature of haptens, carriers and respective antibodies. For structure similarity comparison of haptens, the database also integrates tools like JME Editor and JMOL for sketching, displaying and manipulating hapten 2D/3D structures online. So the database would be of great help in identifying functional group(s) in smaller molecules using antibodies as well as for the development of immunodiagnostics/therapeutics by providing data and procedures available so far for the generation of specific or cross-reactive antibodies. Availability: HaptenDB is available on http://www.imtech.res.in/raghava/haptendb/ and http://bioinformatics.uams.edu/raghava/haptendb/ (Mirror site)

Assessment of different methods of rice (Oryza sativa. L) cultivation affecting growth parameters, soil chemical, biological, and microbiological properties, water saving, and grain yield in rice–rice system

Field experiments were conducted at DRR farm located at ICRISAT, Patancheru, in sandy clay loam soils during four seasons, Kharif 2008, Rabi 2008–2009, Kharif 2009 and Rabi 2009–2010, to investigate growth parameters, water-saving potential, root characteristics, chemical, biological, and microbial properties of rhizosphere soil, and grain yield of rice (Oryza sativa L.) by comparing the plants grown with system of rice intensification (SRI) methods, with organic or organic + inorganic fertilization, against current recommended best management practices (BMP). All the growth parameters including plant height, effective tillers (10–45 %), panicle length, dry matter, root dry weight (24–57 %), and root volume (10–66 %) were found to be significantly higher with in SRI-organic + inorganic over BMP. With SRI-organic fertilization, growth parameters showed inconsistent results; however, root dry weight (3–77 %) and root volume (31–162 %) were found significantly superior compared to BMP. Grain yield was found significantly higher in SRI-organic + inorganic (12–23 and 4–35 % in the Kharif and Rabi seasons, respectively), while with SRI-organic management, yield was found higher (4–34 %) only in the Rabi seasons compared to BMP. An average of 31 and 37 % of irrigation water were saved during Kharif and Rabi seasons, respectively, with both SRI methods of rice cultivation compared to BMP. Further, total nitrogen, organic carbon%, soil dehydrogenase, microbial biomass carbon, total bacteria, fungi, and actinomycetes were found higher in the two SRI plots in comparison to BMP. It is concluded that SRI practices create favorable conditions for beneficial soil microbes to prosper, save irrigation water, and increase grain yield

SRI-A Method for Sustainable Intensification of Rice Production with Enhanced Water Productivity

Climate change induced higher temperatures will increase crops’ water requirements. Every 10°C increase in mean temperature, results in 7% decline in the yield of rice crop. Hence, there is a need to develop water saving technologies in rice which consumes more than 50% of the total irrigation water in agriculture. System of Rice Intensification (SRI) is one such water saving rice production technology. Experiments were conducted at different locations in India including research farm of Directorate of Rice Research (DRR), Hyderabad, during 2005-10 to assess the potential of SRI in comparison to normal transplanting/Standard Planting (NTP/SP) under flooded condition. SRI recorded higher grain yield (6 to 65% over NTP) at majority of locations. Long term studies clearly indicated that grain yield was significantly higher (12-23% and 4-35% over NTP in Kharif and Rabi seasons, respectively) in SRI (with organic+inorganic fertilizers) while the SRI (with100% organic manures), recorded higher yield (4-34%) over NTP only in the Rabi seasons. Even though, SRI resulted in higher productivity, the available nutrient status in soil was marginally higher (10, 42 and 13% over NTP for N, P and K, respectively) at the end of four seasons. There was a reduction in the incidence of pests in SRI and the relative abundance of plant parasitic nematodes was low in SRI as compared to the NTP. About 31% and 37% saving in irrigation water was observed during Kharif and Rabi seasons, respectively in both methods of SRI cultivation over NTP. SRI performed well and consistently reduced requirement of inputs such as seed and water in different soil conditions. SRI method, using less water for rice production can help in overcoming water shortage in future and it can also make water available for growing other crops thus promoting crop diversificatio

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Not AvailableRice (Oryza sativa) is the staple food of Southeast Asian population. Rice is the source of livelihood for hundreds of millions of house holds around the Globe. Several Asian and African countries are highly dependent on rice as a source of food and foreign exchange and government revenue (www.fao.org). Global rice production must increase by 36% by 2025 to feed an estimated 4 billion rice consumers (Pinstrup Anderson et al., 1997). Water scarcity prevails in rice growing areas (Tuong et al., 2005) and societal demands for water from the urban and commercial sectors will continue to increase. In response to rising production costs; especially for labor and water resources, farmers are shifting the methods of crop establishment from traditional transplanting to direct seeding. But direct seeding of rice faces severe challenges from weeds which are a major deterrent in increasing the rice production and productivity. Integrating preventive and interventional methods are essential to manage the weed communities. (Raoet. al., 2007) and improved weed management will be quite crucial. Over 1800 plant species have been reported as weeds of rice in South and South east Asia (Moody 1989) and there is an enormous diversity of taxa considered to be weeds of rice (Soerjani et. al., 1987) Since rice is grown over a wide range of agro ecosystems, such as flooded fully or partially (irrigated) uplands which are highly prove for weed Infestation. In many developing countries, rice farming relies on manual labour and weed control is inefficient leading to their persistence. Weeds compete with the rice plants for nutrients, moisture, sunlight and space, causing a quantitative reduction in the potential yield of rice.Not Availabl

BIOINFORMATICS APPLICATIONS NOTE Databases and ontologies

proteins and anti-hapten antibodie

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Not AvailableThere is a close relationship among agriculture, economics, energy and the environment. A comparison was made between conventional and the system of rice intensification (SRI) methods of rice cultivation by conducting two experiments. One field experiment was conducted from 2013 to 2017 at 25 locations across India under the All India Coordinated Rice Improvement Project and another experiment was conducted in 2017 using surveys by collecting data from 262 randomly selected SRI farmers using a personal interview method in the Telangana state of India. The 5-year experimental data revealed that the SRI method of cultivation produced higher rice grain yield (up to 55%) compared to the conventional transplanting method. Survey data revealed that total costs of rice production reduced by 22.71% under SRI. Break even output under SRI was reduced by 58.1%. Adoption of SRI saved total energy inputs by 4350 MJ/ha. The energy productivities were 0.16 kg/MJ and 0.21 kg/MJ for conventional and SRI methods, respectively. Also, SRI resulted the lowest greenhouse gas emissions of 0.280 kg CO2e/kg rice grain. Therefore, for ensuring higher productivity, net returns, energy efficiency and sustainable rice production it is recommended to adopt an environmentally friendly SRI method of crop establishment in the Telangana region of India.Not Availabl

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Not AvailableThere is a close relationship among agriculture, economics, energy and the environment. A comparison was made between conventional and the system of rice intensification (SRI) methods of rice cultivation by conducting two experiments. One field experiment was conducted from 2013 to 2017 at 25 locations across India under the All India Coordinated Rice Improvement Project and another experiment was conducted in 2017 using surveys by collecting data from 262 randomly selected SRI farmers using a personal interview method in the Telangana state of India. The 5-year experimental data revealed that the SRI method of cultivation produced higher rice grain yield (up to 55%) compared to the conventional transplanting method. Survey data revealed that total costs of rice production reduced by 22.71% under SRI. Break even output under SRI was reduced by 58.1%. Adoption of SRI saved total energy inputs by 4350 MJ/ ha. The energy productivities were 0.16 kg/MJ and 0.21 kg/MJ for conventional and SRI methods, respectively. Also, SRI resulted the lowest greenhouse gas emissions of 0.280 kg CO2 e/kg rice grain. Therefore, for ensuring higher productivity, net returns, energy efficiency and sustainable rice production it is recommended to adopt an environmentally friendly SRI method of crop establishment in the Telangana region of India.Not Availabl

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Not AvailableRice (Orzya sativa L.) is one of the important staple food crops for more than half of the world and is being grown in most of the countries in the world. Varietal improvement and identification of novel sources for low nitrogen and phosphorus (N and P) tolerance helps in reducing the application of these fertilizers, import burdens, and environmental contaminations due to fertilizer run–offs and for getting sustainable yields, thus enhancing the income of farmers. Various novel biotechnology tools such as quantitative trait loci (QTL) mapping, Marker–assisted selection, Genome–Wide Association mapping (GWAS) and Genome editing techniques are discussed in this paper. At the ICAR–Indian Institute of Rice Research, in addition to screening genotypes for higher nutrient–use efficiency, lot of studies were carried out on genetic improvement of rice for development efficient genotypes in rice to minimize the application of fertilizers, which is not only necessary for increasing farmers’ income by saving on the cost of fertilizers but also to sustain the rice production.Not Availabl